aherbert / gdsc-smlm-ij-example-plugin

Example project for an ImageJ plugin using the GDSC SMLM library

This is an example Maven project implementing an ImageJ 1.x plugin that uses the GDSC SMLM ImageJ library.

This is based on the example for an original ImageJ plugin, see: https://github.com/imagej/example-legacy-plugin.

For an example Maven project implementing an ImageJ2 command, see: https://github.com/imagej/example-imagej2-command

It is intended as an ideal starting point to develop new ImageJ 1.x plugins in an IDE of your choice. You can even collaborate with developers using a different IDE than you.

• In Eclipse, for example, it is as simple as File › Import... › Existing Maven Project.

• In NetBeans, it is even simpler: File › Open Project.

• The same works in IntelliJ.

• If jEdit is your preferred IDE, you will need the Maven Plugin.

Die-hard command-line developers can use Maven directly by calling mvn in the project root.

However you build the project, in the end you will have the .jar file (called artifact in Maven speak) in the target/ subdirectory.

To copy the artifact into the correct place, you can call

mvn -Dscijava.app.directory="/path/to/ImageJ.app/"

This will not only copy your artifact, but also all the dependencies. Restart your ImageJ or call Help › Refresh Menus to see your plugin in the menus.

Developing code in an IDE is convenient, especially for debugging. To that end, the plugin contains a main method which sets the plugins.dir system property and adds the plugin to the Plugins menu, starts ImageJ, and runs the plugin. See also this page for information how ImageJ makes it easier to debug in IDEs.

This project is intended as a starting point for your own developments.

How to use this project as a starting point

1. Visit this link to create a new repository in your space using this one as a template.

2. Clone your new repository.

3. Edit the pom.xml file, fixing all the lines labelled FIXME. In particular, change

   1. the artifactId (NOTE: should contain a '_' character)
   2. the groupId, ideally to a reverse domain name your organization owns
   3. the version (note that you typically want to use a version number ending in -SNAPSHOT to mark it as a work in progress rather than a final version)
   4. the dependencies (read how to specify the correct groupId/artifactId/version triplet here)
   5. the developer information
   6. the scm information

4. Remove the example .java files and add your own .java files to src/main/java/<package>/ (if you need supporting files -- like icons -- in the resulting .jar file, put them into src/main/resources/)

5. Edit src/main/resources/plugins.config

6. Replace the contents of README.md with information about your project.

7. Make your initial commit and push the results!

Eclipse: To ensure that Maven copies the plugin to your ImageJ folder

1. Go to Run Configurations...
2. Choose Maven Build
3. Add the following parameter:
   • name: scijava.app.directory
   • value: /path/to/ImageJ.app/

This ensures that the final .jar file will also be copied into your ImageJ plugins folder everytime you run the Maven build.